I do not know on how they derived the resp charges; it is better to read
the paper to know how they did it. But if they did a quantum mechanical
optimization on the structure and followed the resp protocol, then the
charges are resp charges. If your HEME residue is similar to the HEME
structure they used in the paper, yes, you can use these charges in your
simulations as resp charges.
Best,
On Tue, 6 Nov 2007, snoze pa wrote:
> Dear Ilya and David,
> Thanks a lot for your reply.
>
> Ilya, so you i can use those charges directly?
>
> thanks a lot in advance
> s
>
> On Nov 6, 2007 11:36 AM, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:
>
> > If you use antechamber to calculate the charges, they wont be resp
> > charges. For HEME, the parameters are already calculated. Look at the
> > following site:
> >
> > http://pharmacy.man.ac.uk/amber/
> >
> > My rule of thumb is not to calculate something if it is already done. Use
> > the HEME parameters from the above site.
> >
> > Best,
> >
> > On Tue, 6 Nov 2007, snoze pa wrote:
> >
> > > Dear Amber community,
> > > I am working on a heme protein and wondering if I can calculate the
> > charges
> > > on HEME using antechamber. If anybody has any prior experience in this
> > then
> > > please let me know.
> > > thanks in advance.
> > > s
> > >
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > = Department of Chemistry - =
> > = University of Rochester - =
> > = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> > = http://www.pas.rochester.edu/~yildirim/<http://www.pas.rochester.edu/%7Eyildirim/> =
> > ---------------------------------------------------------------
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
--
Ilyas Yildirim
---------------------------------------------------------------
= Department of Chemistry - =
= University of Rochester - =
= Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
= http://www.pas.rochester.edu/~yildirim/ =
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 07 2007 - 06:07:50 PST
